All boats using Port of Salem waters or mooring in its slips, whether rented or owned, are permitted by the Port of Salem Harbormaster Department. Boaters who own their own moorings must have the work done by an authorized mooring company.

The waters of the Port of Salem are divided into six mooring fields. Area "S" stretches from the Beverly Bridge in the Danvers River to Kernwood Bridge. This area has a long waiting list and little turn-over. Area "A," from Monument Bar to Beverly Bridge, is primarily used by two yacht clubs, the Salem Willows and Jubilee Yacht Clubs. Again, there is little available space in area "A," and it has limited access from the Port of Salem shore.

The Port of Salem's Area "L" goes from Winter Island Light to Monument Bar. While there is space available in this Port of Salem mooring area, exposure to bad weather and poor access discourage mooring here.

Area "WI" in the Port of Salem is from the Power Plant Jetty to Winter Island Light has good access from Winter Island Park and plenty of available space. Non-residents must pay an entry fee to the park. Boaters can get annual launch service and a parking pass for $500. The Hawthorne Cove Marina manages the launch.

With limited available space and poor access, the Port of Salem Area "E" stretches from Derby Wharf Light to the Power Plant Jetty. Stretching from Forest River to Derby Light, Area "M" in the Port of Salem has some room available, but access is poor and the water there is shallow.

Except for Area "S," Port of Salem waters are exposed to the phenomenon of the "Nor'easter." While they are rare in the summer, Nor'easters are common in the spring and fall.

The 28-meter (92-foot) Salem Ferry has been operating since 2006, providing ferry service between the Port of Salem and Boston. Running from late spring until the early fall, the ferry ride lasts less than an hour. The Port of Salem Ferry is enclosed and has a snack bar and restrooms. Due to the rising cost of fuel, the Port of Salem Ferry began eliminated its commuter service. In 2011, the service was available from Friday until Sunday through Halloween.

The Port of Salem Wharf project was announced by the mayor in late 2010. The Salem Wharf project involves the build-out of today's Blaney Street Pier to provide space for small- and medium-sized cruise ships, the Salem Ferry, and commercial vessels. The project includes a terminal building with a waiting room and indoor restrooms for the Port of Salem Ferry. It will also have a 140-space paved parking lot, replacing the old dirt parking lot. A long seawall will also be built at the Port of Salem's Blaney Street Landing. The Salem Wharf project is expected to be completed by 2014.